Merge pull request #33 from dpryan79/operator_precedance

Fix some compiler warnings and test logic

pyDNase/footprinting/WellingtonC.h

@@ -188,7 +188,7 @@ struct tuple2 * wellington(unsigned int const * const f,  unsigned int const * c
 				unsigned const int xBackward = b_bindingArray[i+halffpround+1];
 				unsigned const int nBackward = xBackward + rv_fpscores[i-halffpround];
 
-				if (xForward > 0 & xBackward > 0)
+				if (xForward > 0 && xBackward > 0)
 				{
 					float const p = (float)shoulder / (shoulder + fp_size);
 					float const score = bdtrc(xForward - 1, nForward, p) + bdtrc(xBackward - 1, nBackward, p);
@@ -238,7 +238,7 @@ struct tuple2 * wellington1D(unsigned int const * const f,  unsigned int const *
 				unsigned const int xBackward = b_bindingArray[i+halffpround+1];
 				unsigned const int nBackward = xBackward + rv_fpscores[i-halffpround];
 
-				if (xForward > 0 & xBackward > 0)
+				if (xForward > 0 && xBackward > 0)
 				{
 					float const p = (float)(shoulder*2) / ((shoulder*2) + fp_size);
 					float const score = bdtrc(xForward + xBackward - 1, nForward + nBackward, p);
@@ -367,7 +367,7 @@ struct tuple2 * diff_wellington(unsigned int const * const f,  unsigned int cons
 
 //        float t_score = 0.0;
 //
-//        if (xForwardt > 0 & xBackwardt > 0)
+//        if (xForwardt > 0 && xBackwardt > 0)
 //        {
 //            float const p = (float)shoulder / (shoulder + fp_size);
 //            t_score = bdtrc(xForwardt - 1, nForwardt, p) + bdtrc(xBackwardt - 1, nBackwardt, p);
@@ -395,7 +395,7 @@ struct tuple2 * diff_wellington(unsigned int const * const f,  unsigned int cons
 
             float prior_score;
 
-            if (xForward > 0 & xBackward > 0)
+            if (xForward > 0 && xBackward > 0)
             {
                 const float p = (float)shoulder / (shoulder + fp_size);
                 prior_score = bdtrc(xForward - 1, nForward, p) + bdtrc(xBackward - 1, nBackward, p);
@@ -417,7 +417,7 @@ struct tuple2 * diff_wellington(unsigned int const * const f,  unsigned int cons
                 unsigned const int nForward  = slice(t_f2,0,shoulder + fp_size);
                 unsigned const int xBackward = slice(t_r2,shoulder + fp_size,shoulder + shoulder + fp_size);
                 unsigned const int nBackward = slice(t_r2,shoulder,shoulder + shoulder + fp_size);
-                if (xForward > 0 & xBackward > 0)
+                if (xForward > 0 && xBackward > 0)
                 {
                     float const p = (float)shoulder / (shoulder + fp_size);
                     bootstrap_score[i] = bdtrc(xForward - 1, nForward, p) + bdtrc(xBackward - 1, nBackward, p);
@@ -448,4 +448,4 @@ struct tuple2 * diff_wellington(unsigned int const * const f,  unsigned int cons
 	retarr->fpscores = scores;
 	retarr->mles = mle;
 	return retarr;
-}
+}

pyDNase/scripts/dnase_average_profile.py

@@ -1,3 +1,4 @@
+#!/usr/bin/env python
 import argparse
 import pyDNase
 import numpy as np

pyDNase/scripts/dnase_bias_estimator.py

@@ -1,3 +1,4 @@
+#!/usr/bin/env python
 import os, argparse, tempfile, operator, pickle
 from collections import defaultdict
 import pybedtools, pysam

pyDNase/scripts/dnase_cut_counter.py

@@ -1,3 +1,4 @@
+#!/usr/bin/env python
 import argparse
 import pyDNase
 from clint.textui import progress, puts

pyDNase/scripts/dnase_ddhs_scorer.py

@@ -1,3 +1,4 @@
+#!/usr/bin/env python
 import argparse
 import pyDNase
 import math

pyDNase/scripts/dnase_fos_scorer.py

@@ -1,3 +1,4 @@
+#!/usr/bin/env python
 import argparse
 import pyDNase
 from clint.textui import progress

pyDNase/scripts/dnase_pretty_picture.py

@@ -1,3 +1,4 @@
+#!/usr/bin/env python
 __author__ = "Jason Piper"
 
 """
@@ -134,4 +135,4 @@
 
 plt.tight_layout()
 plt.savefig(args.output)
-#plt.show()
+#plt.show()

pyDNase/scripts/dnase_to_JSON.py

@@ -1,3 +1,4 @@
+#!/usr/bin/env python
 import argparse, pyDNase
 from clint.textui import puts, progress
 parser = argparse.ArgumentParser(description='Writes a JSON file of DNase I cuts for regions from a BED file')

pyDNase/scripts/dnase_to_javatreeview.py

@@ -1,3 +1,4 @@
+#!/usr/bin/env python
 import argparse, pyDNase, csv, random
 import numpy as np
 from clint.textui import puts, progress
@@ -80,4 +81,4 @@ def normalise_cuts(cuts):
 
         newarray = np.subtract(cuts["+"], cuts["-"])
 
-    outfile.writerow(["NULL","NULL",i.chromosome + ":" + str(i.startbp) + ":" + str(i.endbp)] + newarray.tolist())
+    outfile.writerow(["NULL","NULL",i.chromosome + ":" + str(i.startbp) + ":" + str(i.endbp)] + newarray.tolist())

pyDNase/scripts/dnase_wig_tracks.py

@@ -1,3 +1,4 @@
+#!/usr/bin/env python
 import argparse
 from clint.textui import progress, puts
 import pyDNase
@@ -38,4 +39,4 @@
             print(-i, file=bwigout)
 
 fwigout.close()
-bwigout.close()
+bwigout.close()

pyDNase/scripts/wellington_bootstrap.py

@@ -1,3 +1,4 @@
+#!/usr/bin/env python
 import pyDNase, pyDNase.footprinting
 import numpy as np
 from clint.textui import progress

pyDNase/scripts/wellington_footprints.py

@@ -1,3 +1,4 @@
+#!/usr/bin/env python
 import multiprocessing as mp
 import argparse, os
 from clint.textui import progress, puts_err

setup.py

@@ -26,6 +26,7 @@
 
     install_requires=[
         # Not enforcing versions for numpy as it can be a bitch to upgrade
+        "Cython",
         "numpy", # Tested on >=1.5.0
         "matplotlib < 2.0.0", # mpl > 2.0 only works on py3
         "pysam >= 0.8.1",
@@ -47,4 +48,4 @@
         "pyDNase/scripts/dnase_to_JSON.py",
         "pyDNase/scripts/dnase_bias_estimator.py"],
     test_suite="test",
-)
+)